Database Resources of the National Genomics Data Center in 2020

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems, including the constituent elements within and among species. Through various efforts in genomic data archiving, integrative analysis and value-added curation, the National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), has successfully established and currently maintains a vast amount of database resources. This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts. Here, we present a comprehensive overview of central repositories dedicated to archiving, presenting, and sharing plant omics data, introduce knowledgebases focused on variants or gene-based functional insights, highlight species-specific multiple omics database resources, and briefly review the online application tools. We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-023-00134-4.

The mediation effect of glucocorticoid receptor gene (NR3C1) methylation between childhood maltreatment and depressive symptoms in Chinese adolescents: A 2-year longitudinal study

This three-wave longitudinal study examined whether methylation alterations in promoter exon 1F of a stress-related gene-NR3C1 (NR3C1-1F)-explained the longitudinal associations between childhood maltreatment and adolescent depressive symptoms. A total of 370 Han Chinese adolescents (Mage  = 16.31 ± 1.28 years; 51.4% girls) recruited from Shandong, China were tracked from 2018 to 2020. The results showed that the severity of childhood maltreatment, especially that of emotional abuse and physical neglect, conferred risk for adolescent depressive symptoms via reducing NR3C1-1F methylation levels. These mediation effects of NR3C1-1F methylation did not vary between adolescent sex or NR3C1 BclI and Tth111I polymorphisms. The findings highlight how childhood maltreatment contributes to psychopathology development at a biological level.

Bovine Omasum-Inspired Interfacial Carbon-Based Nanocomposite for Saliva Metabolic Screening of Gastric Cancer

Gastric cancer is one of the most common malignant digestive cancers, and its diagnostic has still faced challenges based on metabolic analysis due to complex sample pretreatment and low metabolite abundance. In this study, inspired by the structure of bovine omasum, we in situ synthesized a novel interfacial carbon-based nanocomposite of graphene supported nickel nanoparticles-encapsulated in the nitrogen-doped carbon nanotube (Ni/N-CNT/rGO), which was served as a novel matrix with enhanced ionization efficiency for the matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) saliva metabolic analysis of gastric cancer. Benefiting from its high sp² graphitic degree, large surface area, strong UV absorption, and rich active sites, Ni/N-CNT/rGO matrix exhibited excellent performances of reproducibility, coverage, salt-tolerance, sensitivity, and adsorption ability in MALDI-TOF MS. The differential scanning calorimetry (DSC) and thermal conversion behaviors explained the highly efficient LDI mechanism. Based on saliva metabolic fingerprints, Ni/N-CNT/rGO assisted LDI MS with cross-validation analysis could successfully distinguish gastric cancer patients from healthy controls through the screening of four potential biomarkers with an accuracy of 92.50%, specificity of 88.03%, and sensitivity of 97.12%. This work provided a fast and sensitive MS sensing platform for the metabolomics characterization of gastric cancer and might have potential value for precision medicine in the future.

Multilineage contribution of CD34+ cells in cardiac remodeling after ischemia/reperfusion injury

The ambiguous results of multiple CD34+ cell-based therapeutic trials for patients with heart disease have halted the large-scale application of stem/progenitor cell treatment. This study aimed to delineate the biological functions of heterogenous CD34+ cell populations and investigate the net effect of CD34+ cell intervention on cardiac remodeling. We confirmed, by combining single-cell RNA sequencing on human and mouse ischemic hearts and an inducible Cd34 lineage-tracing mouse model, that Cd34+ cells mainly contributed to the commitment of mesenchymal cells, endothelial cells (ECs), and monocytes/macrophages during heart remodeling with distinct pathological functions. The Cd34+-lineage-activated mesenchymal cells were responsible for cardiac fibrosis, while CD34+Sca-1high was an active precursor and intercellular player that facilitated Cd34+-lineage angiogenic EC-induced postinjury vessel development. We found through bone marrow transplantation that bone marrow-derived CD34+ cells only accounted for inflammatory response. We confirmed using a Cd34-CreERT2; R26-DTA mouse model that the depletion of Cd34+ cells could alleviate the severity of ventricular fibrosis after ischemia/reperfusion (I/R) injury with improved cardiac function. This study provided a transcriptional and cellular landscape of CD34+ cells in normal and ischemic hearts and illustrated that the heterogeneous population of Cd34+ cell-derived cells served as crucial contributors to cardiac remodeling and function after the I/R injury, with their capacity to generate diverse cellular lineages.

Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker

The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00165-2.

Detection of multiple types of cancer driver mutations using targeted RNA sequencing in nonsmall cell lung cancer

BACKGROUND

DNA-based next-generation sequencing has been widely used in the selection of target therapies for patients with nonsmall cell lung cancer (NSCLC). RNA-based next-generation sequencing has been proven to be valuable in detecting fusion and exon-skipping mutations and is recommended by National Comprehensive Cancer Network guidelines for these mutation types.

METHODS

The authors developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for the detection of fusions, single-nucleotide variants (SNVs), and insertion/deletion (indels). In total, 1253 formalin-fixed, paraffin-embedded samples from patients with NSCLC were analyzed by DNA and RNA panel sequencing in parallel to assess the performance of the RNA panel in detecting multiple types of mutations.

RESULTS

In analytical validation, the RNA panel achieved a limit of detection of 1.45-3.15 copies per nanogram for SNVs and 0.21-6.48 copies per nanogram for fusions. In 1253 formalin-fixed, paraffin-embedded NSCLC samples, the RNA panel identified a total of 124 fusion events and 26 MET exon 14-skipping events, in which 14 fusions and six MET exon 14-skipping mutations were missed by DNA panel sequencing. By using the DNA panel as the reference, the positive percent agreement and the positive predictive value of the RNA panel were 98.08% and 98.62%, respectively, for detecting targetable SNVs and 98.15% and 99.38%, respectively, for detecting targetable indels.

CONCLUSIONS

Parallel DNA and RNA sequencing analyses demonstrated the accuracy and robustness of the RNA sequencing panel in detecting multiple types of clinically actionable mutations. The simplified experimental workflow and low sample consumption will make RNA panel sequencing a potentially effective method in clinical testing.

Phenotypes and genetic etiology of spontaneous polycystic kidney and liver disease in cynomolgus monkey

Introduction

Polycystic kidney disease (PKD) is a common autosomal dominant or recessive genetic disease, often accompanied by polycystic liver disease (PLD). Many cases of PKD in animals have been reported. However, little is known about the genes that cause PKD in animals.

Methods

In this study, we evaluated the clinical phenotypes of PKD in two spontaneously aged cynomolgus monkeys and explored the genetic etiology using whole-genome sequencing (WGS). Ultrasonic and histological consequences were further investigated in PKD- and PLD-affected monkeys.

Results

The results indicated that the kidneys of the two monkeys had varying degrees of cystic changes, and the renal cortex was thinned and accompanied by fluid accumulation. As for hepatopathy, inflammatory cell infiltration, cystic effusion, steatosis of hepatocytes, and pseudo-lobular were found. Based on WGS results, the variants of PKD1:(XM_015442355: c.1144G>C p. E382Q) and GANAB: (NM_001285075.1: c.2708T>C/p. V903A) are predicted to be likely pathogenic heterozygous mutations in PKD- and PLD-affected monkeys.

Discussion

Our study suggests that the cynomolgus monkey PKD and PLD phenotypes are very similar to those in humans, and are probably caused by pathogenic genes homologous to humans. The results indicate that cynomolgus monkeys can be used as the most appropriate animal model for human PKD pathogenesis research and therapeutic drug screening.

Significant Differences in Planktonic Virus Communities Between "Cellular Fraction" (0.22 ~ 3.0 µm) and "Viral Fraction" (< 0.22 μm) in the Ocean

Compared to free-living viruses (< 0.22 m) in the ocean, planktonic viruses in the "cellular fraction" (0.22 ~ 3.0 μm) are now far less well understood, and the differences between them remain largely unexplored. Here, we revealed that even in the same seawater samples, the "cellular fraction" comprised significantly distinct virus communities from the free virioplankton, with only 13.87% overlap in viral contigs at the species level. Compared to the viral genomes deposited in NCBI RefSeq database, 99% of the assembled viral genomes in the "cellular fraction" represented novel genera. Notably, the assembled (near-) complete viral genomes within the "cellular fraction" were significantly larger than that in the "viral fraction," and the "cellular fraction" contained three times more species of giant viruses or jumbo phages with genomes > 200 kb than the "viral fraction." The longest complete genomes of jumbo phage (~ 252 kb) and giant virus (~ 716 kb) were both detected only in the "cellular fraction." Moreover, a relatively higher proportion of proviruses were predicted within the "cellular fraction" than "viral fraction." Besides the substantial divergence in viral community structure, the different fractions also contained their unique viral auxiliary metabolic genes; e.g., those potentially participating in inorganic carbon fixation in deep sea were detected only in the "cellular-fraction" viromes. In addition, there was a considerable divergence in the community structure of both "cellular fraction" and "viral fraction" viromes between the surface and deep-sea habitats, suggesting that they might have similar environmental adaptation properties. The findings deepen our understanding of the complexity of viral community structure and function in the ocean.

The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments

How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.

Integrated chromatin accessibility and DNA methylation analysis to reveal the critical epigenetic modification and regulatory mechanism in gonadal differentiation of the sequentially hermaphroditic fish, Monopterus albus

BACKGROUND

Monopterus albus is a hermaphroditic and economically farmed fish that undergoes sex reversal from ovary to testis via ovotestis during gonadal development. The epigenetic changes that are associated with gonadal development in this species remain unclear.

METHODS

We produced DNA methylome, transcriptome, and chromatin accessibility maps of the key stages of gonad development: ovary, ovotestis, and testis. The expression of the key candidate genes was detected using qRT-PCR and in situ hybridization and the methylation levels were analysed using bisulphite sequencing PCR. Promoter activity and regulation were assessed using dual-luciferase reporter assays.

RESULTS

Gonadal development exhibits highly dynamic transcriptomic, DNA methylation, and chromatin accessibility changes. We found that DNA methylation status, especially of the transcription start site, was significantly negatively correlated with gene expression while chromatin accessibility exhibited no correlation with gene expression during gonadal development. The epigenetic signatures revealed many novel regulatory elements and genes involved in sex reversal, which were validated. DNA methylation detection and site mutation of plastin-2 promoter, as a candidate gene, revealed that DNA methylation could impact the binding of transcription factor dmrt1 and foxl2 through methylation and demethylation to regulate plastin-2 expression during gonadal development.

CONCLUSIONS

These data provide novel insights into epigenetic modification and help elucidate the potential molecular mechanism by which dynamic modification of DNA methylation plays a crucial role in gonadal development.

Frequent exacerbators of chronic obstructive pulmonary disease have distinguishable sputum microbiome signatures during clinical stability

INTRODUCTION

Frequent exacerbation phenotype of chronic obstructive pulmonary disease (COPD) represents a more concerning disease subgroup requiring better prevention and intervention, of which airway microbiome provides new perspective for further exploration.

METHODS

To investigate whether frequent exacerbators of COPD have distinguishable sputum microbiome during clinical stability, COPD patients at high disease grades with or without frequent exacerbation were recruited for sputum microbiome analysis. Sputum samples were collected during clinical stability and underwent 16S rRNA sequencing, which was then subjected for amplicon sequence variants (ASVs)-based microbiome analysis.

RESULTS

Our results revealed that compared with healthy controls and infrequent exacerbators, frequent COPD exacerbators have distinguishably dysbiotic sputum microbiome, as featured by fewer ASVs features, lower alpha diversity, distinct beta diversity patterns. Further taxonomic compositional analysis illustrated the structural distinctions between frequent COPD exacerbators and infrequent exacerbators at differential taxa levels and highlighted Stenotrephomonas due to its prominent elevation in frequent COPD exacerbators, providing a promising candidate for further exploration of microbiome biomarker. Moreover, we also demonstrated that frequent exacerbation phenotype is distinguishable from infrequent exacerbation phenotype with respect of functional implications.

CONCLUSION

Our study demonstrated the first positive correlation between the frequent exacerbation phenotype of COPD and the sputum microbiome during clinical stability in a single-center Chinese COPD cohort and provide potential diagnostic and therapeutic targets for further investigation.

Pin-Pointing the Key Hubs in the IFN-γ Pathway Responding to SARS-CoV-2 Infection

Interferon gamma (IFN-γ) may be potential adjuvant immunotherapy for COVID-19 patients. In this work, we assessed gene expression profiles associated with the IFN-γ pathway in response to SARS-CoV-2 infection. Employing a case-control study from SARS-CoV-2-positive and -negative patients, we identified IFN-γ-associated pathways to be enriched in positive patients. Bioinformatics analyses showed upregulation of MAP2K6, CBL, RUNX3, STAT1, and JAK2 in COVID-19-positive vs. -negative patients. A positive correlation was observed between STAT1/JAK2, which varied alongside the patient’s viral load. Expression of MX1, MX2, ISG15, and OAS1 (four well-known IFN-stimulated genes (ISGs)) displayed upregulation in COVID-19-positive vs. -negative patients. Integrative analyses showcased higher levels of ISGs, which were associated with increased viral load and STAT1/JAK2 expression. Confirmation of ISGs up-regulation was performed in vitro using the A549 lung cell line treated with Poly (I:C), a synthetic analog of viral double-stranded RNA; and in different pulmonary human cell lines and ferret tracheal biopsies infected with SARS-CoV-2. A pre-clinical murine model of Coronavirus infection confirmed findings displaying increased ISGs in the liver and lungs from infected mice. Altogether, these results demonstrate the role of IFN-γ and ISGs in response to SARS-CoV-2 infection, highlighting alternative druggable targets that can boost the host response.

Methylophaga pinxianii sp. nov., isolated from the Mariana Trench

Two strains, TMB456T and TMB1265, were isolated from different locations in the Mariana Trench. Analysis of the 16S rRNA gene and genomic rRNA sequences indicated that they were from the same novel species and were affiliated with the genus Methylophaga of the class Gammaproteobacteria . Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Methylophaga muralis Kr3T (98.1 % similarity) and Methylophaga nitratireducenticrescens JAM1T (97.3 % similarity). Digital DNA–DNA hybridization values of TMB456T with M. muralis Kr3T and M. nitratireducenticrescens JAM1T were <25 %. The average nucleotide identity value between strain TMB456T and M. muralis Kr3T was 80.9 %. The genomic DNA G+C contents of strains TMB456T and TMB1265 were both 44.9 mol %. Strains TMB456T and TMB1265 could grow at 4–37 °C (optimum at 20–28 °C), at pH 3–10 (optimum at pH 7–9) and in the presence of 0–10 % (w/v) NaCl (optimum at 0–1 %). Cells of strains TMB456T and TMB1265 were Gram-negative rods (0.3–0.6 µm×0.7–1.3 µm). Chemotaxonomic analysis showed that ubiquinone 8 was the sole quinone produced by strain TMB456T and that the major cellular fatty acids were iso-C16 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipid profile of this strain included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipids and two unidentified polar lipids. Based on the phenotypic, chemotaxonomic and molecular features, strains TMB456T and TMB1265 belong to a novel species within the genus Methylophaga , for which the name Methylophaga pinxianii sp. nov. is proposed. The type strain is TMB456T (=KCTC 82622T= MCCC 1K05898T).

Thalassolituus alkanivorans sp. nov., a hydrocarbon-utilizing bacterium isolated from the Mariana Trench

Two strains, TMPB967T and TTPB476, were isolated from two different locations in the Mariana Trench. Cells of strains TMPB967T and TTPB476 were Gram-negative, curved rod-shaped (0.35–0.6 µm×2–4 µm) with flagella. Both strains were catalase- and oxidase-positive. Strains TMPB967T and TTPB476 could grow at 4–37 °C (optimum, 37 °C), at pH 6–9 (optimum, pH 6–7) and in the presence of 0–8 % (w/v) NaCl (optimum, 5 %). Both strains could grow with tetradecane or hexadecane as the sole carbon source. The predominant isoprenoid quinone was ubiquinone 9. The major cellular fatty acids of strains TMPB967T and TTPB476 were C18 : 1  ω9c, C16 : 0 and summed feature 3 (C16 : 1  ω7c or ω6c). The polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminolipid. The DNA G+C contents of strains TMPB967T and TTPB476 were 53.1 and 53.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Thalassolituus marinus IMCC1826T (97.1 % similarity) and Thalassolituus oleivorans MIL-1T (95.9 % similarity). Digital DNA–DNA hybridization results of strain TMPB967T with TTPB476, T. marinus IMCC1826T and T. oleivorans MIL-1T were 99.9, 20.9 and 20.2 %, respectively. Average nucleotide identity results of strain TMPB967T with TTPB476, T. marinus IMCC1826T and T. oleivorans MIL-1T were 100, 75.8 and 72.0 %, respectively. On the basis of the phenotypic, chemotaxonomic and molecular features, strains TMPB967T and TTPB476 belong to a novel species within the genus Thalassolituus , for which the name Thalassolituus alkanivorans sp. nov. is proposed. The type strain is TMPB967T (=KCTC 82621T=MCCC 1K05476T).

Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China

Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin. Our results show that the populations inhabiting Shimao City had close genetic connections with an earlier population in the Middle Neolithic Yangshao period of northern Shaanxi Province, revealing a mostly local origin for the Shimao Society. In addition, among the populations in other regions of the Yellow River basin, the Shimao-related populations had the closest maternal affinity with the contemporaneous Taosi populations from the Longshan period. The Shimao-related populations also shared more affinity with present-day northern Han populations than with the minorities and southern Han in China. Our study provides a new perspective on the genetic origins and structure of the Shimao people and the population dynamics in the Middle Yellow River basin during the Neolithic period.

Evaluation of the SMARTCHEK Genesystem RT-qPCR assay for the detection of SARS-CoV-2 in clinical samples

BACKGROUND

The COVID-19 pandemic remains the main public health problem, due to the quick and easy dissemination of the causal agent, SARS-CoV-2 virus, around the world. Since the beginning of the pandemic, an opportune laboratory diagnosis has been critical to respond this emergency, and RT-qPCR has been used as reference molecular tests for detection of SARS-CoV-2.

METHODS

In this study, we performed the evaluation of a RT-qPCR SMARTCHEK platform (SMARTCHEK, Genesystem) for SARS-CoV-2 detection based on the amplification of RdRp and N gene markers. The platform was evaluated with nasopharyngeal swab samples corresponding to 360 suspected cases of COVID-19 which were remitted to Instituto Nacional de Salud in Peru. This quick method was compared with conventional RT-qPCR as gold standard.

RESULTS

The RT-qPCR SMARTCHEK showed a 98.1% sensitivity (CI: 93.3-99.8%), a 98.8% specificity (CI: 96.6-99.8%), a 97.2% positive predictive value (CI: 92-99.4%) and a 99.2% negative predictive value (CI: 97.2-99.9%). The assay demonstrated a strong agreement between the RT-qPCR SMARTCHEK and conventional RT-qPCR (kappa value ≥ 0.966).

CONCLUSION

The RT-qPCR SMARTCHEK is a platform that gives reliable and fast results, with high sensitivity and specificity for the detection of SARS-CoV-2, and it will be considered a suitable alternative to COVID-19 diagnosis in low-resource settings.

Metabolome and transcriptome analyses identify the plant immunity systems that facilitate sesquiterpene and lignan biosynthesis in Syringa pinnatifolia Hemsl

BACKGROUND

Syringa pinnatifolia Hemsl. is a shrub belonging to the Oleaceae family. The peeled woody stems and roots of S. pinnatifolia are used in Chinese traditional medicine. This plant has been used for centuries, and modern pharmacological research has revealed its medicinal value. However, the wild populations of S. pinnatifolia have been decreasing, and it has been listed as an endangered plant in China. To elucidate the molecular mechanism leading to the synthesis of the major components of S. pinnatifolia for its further development and sustainable use, this study compared peeled stems and twigs at the metabolic and molecular levels.

RESULTS

Peeled stems with the purple substance visible (SSP) and peeled twigs without the purple substance (TSP) were compared at different levels. Microscopic observation showed resin-like fillers in SSP and wood fiber cell walls approximately 1.0 μm thicker than those in TSP (wood fiber cell thickness approximately 2.7 μm). In addition, 104 volatile organic compounds and 870 non-volatile metabolites were detected in the non-targeted and widely-targeted metabolome analyses, respectively. Among the 76 differentially accumulated metabolites (DAMs) detected, 62 were up-accumulated in SSP. Most of these DAMs were terpenes, of which 90% were identified as sesquiterpenes in the volatile organic compound analysis. In the analysis of the non-volatile metabolites, 21 differentially accumulated lignans were identified, of which 18, including five subtypes, were accumulated in SSP. RNA sequencing revealed 4,421 upregulated differentially expressed genes (DEGs) and 5,522 downregulated DEGs in SSP compared with TSP, as well as 33,452 genes that were not differentially expressed. Analysis of the DEGs suggested that sesquiterpenes and lignans were mostly biosynthesized via the mevalonate and phenylpropanoid pathways, respectively. Additionally, in SSP, the enriched Gene Ontology terms included response to biotic stimulus and defense response, while the enriched Kyoto Encyclopedia of Genes and Genomes pathways included plant-pathogen interaction and many other pathways related to plant immunity.

CONCLUSIONS

This study provides metabolome and transcriptome information for S. pinnatifolia, suggesting that biotic stimuli, including pathogens, are potential and valuable approaches to promoting the biosynthesis of the metabolites linked to the medicinal properties of this plant.

The Spatial Landscape of the Bacterial Community and Bile Acids in the Digestive Tract of Patients With Bile Reflux

Background

Bile reflux can lead to inflammation and increased intestinal metaplasia. Since bile acids can influence the gastrointestinal environment, it is possible that bile reflux may alter the gastric microbiota and potentially the oral or gut microbiota. Bile acids have a very complex interrelationship with microbiota. We aimed to explore the characteristics of the digestive tract microbiota and bile acids profile in bile reflux patients.

Methods

This study included 20 chronic gastritis patients with bile reflux and 20 chronic gastritis patients without bile reflux. Saliva, gastric fluid, and fecal samples were collected for bile acid testing. Buccal mucosal swabs, gastric mucosal tissues, and feces were collected for bacteria detection. The UPLC-MS/MS examined bile acids profiles. 16S rRNA gene sequencing was used to analyze the bacterial profile.

Results

Bilirubin in the blood increased in bile reflux patients. No other clinical factors were identified to be significantly associated with bile reflux. 12-DHCA, 6,7-diketo LCA, and βHDCA decreased while TUDCA increased in saliva of bile reflux patients. Streptococcus, Capnocytophaga, Neisseria, and Actinobacillus decreased in oral mucosa of bile reflux patients while Helicobacter, Prevotella, and Veillonella increased. Gastric bile acid levels were generally higher in bile reflux patients. Gastric mucosal microbiota was highly stable. The changes in fecal bile acids were insignificant. Bifidobacterium, Prevotella_2, Ruminococcus, Weissella, Neisseria, and Akkermansia decreased in fecal samples from bile reflux patients; while Alloprevotella, Prevotella_9, Parabacteroides, and Megamonas increased.

Conclusion

Our results demonstrate that bile reflux significantly alters the oral, gastric, and intestinal bile acids profiles but only influences the oral and gut microbiota composition. These findings indicate that bile reflux can modulate the gastrointestinal microbiota in a site-specific manner.

Vitamin C Deficiency Causes Cell Type-Specific Epigenetic Reprogramming and Acute Tubular Necrosis in a Mouse Model

BACKGROUND

Vitamin C deficiency is found in patients with variable kidney diseases. However, the role of vitamin C as an epigenetic regulator in renal homeostasis and pathogenesis remains largely unknown.

METHODS

We showed that vitamin C deficiency leads to acute tubular necrosis (ATN) using a vitamin C-deficient mouse model (Gulo knock-out). DNA/RNA epigenetic modifications and injured S3 proximal tubule cells were identified in the vitamin C-deficient kidneys using whole-genome bisulfite sequencing, methylated RNA immunoprecipitation sequencing, and single-cell RNA sequencing.

RESULTS

Integrated evidence suggested that epigenetic modifications affected the proximal tubule cells and fenestrated endothelial cells, leading to tubule injury and hypoxia through transcriptional regulation. Strikingly, loss of DNA hydroxymethylation and DNA hypermethylation in vitamin C-deficient kidneys preceded the histologic sign of tubule necrosis, indicating the causality of vitamin C-induced epigenetic modification in ATN. Consistently, prophylactic supplementation of an oxidation-resistant vitamin C derivative, ascorbyl phosphate magnesium, promoted DNA demethylation and prevented the progression of cisplatin-induced ATN.

CONCLUSIONS

Vitamin C played a critical role in renal homeostasis and pathogenesis in a mouse model, suggesting vitamin supplementation may be an approach to lower the risk of kidney injury.

Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.

Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing

This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains.

Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.

Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community

Cerebrospinal fluid (CSF) circulating in the human central nervous system has long been considered aseptic in healthy individuals, because normally, the blood-brain barrier can protect against microbial invasions. However, this dogma has been called into question by several reports that microbes were identified in human brains, raising the question of whether there is a microbial community in the CSF of healthy individuals without neurological diseases. Here, we collected CSF samples and other samples, including one-to-one matched oral and skin swab samples (positive controls), from 23 pregnant women aged between 23 and 40 years. Normal saline samples (negative controls), sterile swabs, and extraction buffer samples (contamination controls) were also collected. Twelve of the CSF specimens were also used to evaluate the physiological activities of detected microbes. Metagenomic and metatranscriptomic sequencing was performed in these 116 specimens. A total of 620 nonredundant microbes were detected, which were dominated by bacteria (74.6%) and viruses (24.2%), while in CSF samples, metagenomic sequencing found only 26 nonredundant microbes, including one eukaryote, four bacteria, and 21 viruses (mostly bacteriophages). The beta diversity of microbes compared between CSF metagenomic samples and other types of samples (except negative controls) was significantly different from that of the CSF self-comparison. In addition, there was no active or viable microbe in the matched metagenomic and metatranscriptomic sequencing of CSF specimens after subtracting those also found in normal saline, DNA extraction buffer, and skin swab specimens. In conclusion, our results showed no strong evidence of a colonized microbial community present in the CSF of healthy individuals. IMPORTANCE The microbiome is prevalent throughout human bodies, with profound health implications. However, it remains unclear whether it is present and active in human CSF, which has been long considered aseptic due to the blood-brain barrier. Here, we applied unbiased metagenomic and metatranscriptomic sequencing to detect the presence of a microbiome in CSF collected from 23 pregnant women with matched controls. Analysis of 116 specimens found no strong evidence to support the presence of a colonized microbiome in CSF. Our findings will strengthen our understanding of the internal environment of the CSF in healthy people, which has strong implications for human health, especially for neurological infections and disorders, and will help further disease diagnostics, prevention, and therapeutics in clinical settings.

Transcriptome Analysis of Neuroendocrine Regulation of Ovine Hypothalamus-Pituitary-Ovary Axis during Ovine Anestrus and the Breeding Season

Most sheep are seasonal estrus, and they breed in autumn when the days get shorter. Seasonal estrus is an important factor that affects the productivity and fertility of sheep. The key point to solve this problem is to explore the regulation mechanism of estrus in sheep. Therefore, in this study, transcriptomic sequencing technology was used to identify differentially expressed mRNAs in the hypothalamus, pituitary and ovary of Small Tail Han sheep (year-round estrus) and tan sheep (seasonal estrus) among luteal, proestrus and estrus stages. There were 256,923,304,156 mRNAs being identified in the hypothalamus, pituitary and ovary, respectively. Functional analysis showed that the photosensor, leucine and isoleucine biosynthesis pathways were enriched significantly. It is speculated that photoperiod may initiate estrus by stimulating the corresponding pathways in hypothalamus. ODC1, PRLH, CRYBB2, SMAD5, OPN1SW, TPH1 are believed to be key genes involved in the estrogen process. In conclusion, this study expanded the database of indigenous sheep breeds, and also provided new candidate genes for future genetic and molecular studies on the seasonal estrus trait in sheep.

Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave

The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5’UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.

Global Diversification and Distribution of Coronaviruses With Furin Cleavage Sites

Knowledge about coronaviruses (CoVs) with furin cleavage sites is extremely limited, although these sites mediate the hydrolysis of glycoproteins in plasma membranes required for MERS-CoV or SARS-CoV-2 to enter cells and infect humans. Thus, we have examined the global epidemiology and evolutionary history of SARS-CoV-2 and 248 other CoVs with 86 diversified furin cleavage sites that have been detected in 24 animal hosts in 28 countries since 1954. Besides MERS-CoV and SARS-CoV-2, two of five other CoVs known to infect humans (HCoV-OC43 and HCoV-HKU1) also have furin cleavage sites. In addition, human enteric coronavirus (HECV-4408) has a furin cleavage site and has been detected in humans (first in Germany in 1988), probably via spillover events from bovine sources. In conclusion, the presence of furin cleavage sites might explain the polytropic nature of SARS-CoV-2- and SARS-CoV-2-like CoVs, which would be helpful for ending the COVID-19 pandemic and preventing outbreaks of novel CoVs.

Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses

Several single-cell RNA sequencing (scRNA-seq) studies analyzing immune response to COVID-19 infection have been recently published. Most of these studies have small sample sizes, which limits the conclusions that can be made with high confidence. By re-analyzing these data in a standardized manner, we validated 8 of the 20 published results across multiple datasets. In particular, we found a consistent decrease in T-cells with increasing COVID-19 infection severity, upregulation of type I Interferon signal pathways, presence of expanded B-cell clones in COVID-19 patients but no consistent trend in T-cell clonal expansion. Overall, our results show that the conclusions drawn from scRNA-seq data analysis of small cohorts of COVID-19 patients need to be treated with some caution.

Catenin α 1 mutations cause familial exudative vitreoretinopathy by overactivating Norrin/β-catenin signaling

Familial exudative vitreoretinopathy (FEVR) is a severe retinal vascular disease that causes blindness. FEVR has been linked to mutations in several genes associated with inactivation of the Norrin/β-catenin signaling pathway, but these account for only approximately 50% of cases. We report that mutations in α-catenin (CTNNA1) cause FEVR by overactivating the β-catenin pathway and disrupting cell adherens junctions. We identified 3 heterozygous mutations in CTNNA1 (p.F72S, p.R376Cfs*27, and p.P893L) by exome sequencing and further demonstrated that FEVR-associated mutations led to overactivation of Norrin/β-catenin signaling as a result of impaired protein interactions within the cadherin-catenin complex. The clinical features of FEVR were reproduced in mice lacking Ctnna1 in vascular endothelial cells (ECs) or with overactivated β-catenin signaling by an EC-specific gain-of-function allele of Ctnnb1. In isolated mouse lung ECs, both CTNNA1-P893L and F72S mutants failed to rescue either the disrupted F-actin arrangement or the VE-cadherin and CTNNB1 distribution. Moreover, we discovered that compound heterozygous Ctnna1 F72S and a deletion allele could cause a similar phenotype. Furthermore, in a FEVR family, we identified a mutation of LRP5, which activates Norrin/β-catenin signaling, and the corresponding knockin mice exhibited a partial FEVR-like phenotype. Our study demonstrates that the precise regulation of β-catenin activation is critical for retinal vascular development and provides new insights into the pathogenesis of FEVR.

Global landscape of SARS-CoV-2 genomic surveillance, public availability extent of genomic data, and epidemic shaped by variants

Genomic surveillance has shaped our understanding of SARS-CoV-2 variants, which have proliferated globally in 2021.We collected country-specific data on SARS-CoV-2 genomic surveillance, sequencing capabilities, public genomic data from multiple public repositories, and aggregated publicly available variant data. Then, different proxies were used to estimate the sequencing coverage and public availability extent of genomic data, in addition to describing the global dissemination of variants. We found that the COVID-19 global epidemic clearly featured increasing circulation of Alpha since the start of 2021, which was rapidly replaced by the Delta variant starting around May 2021. SARS-CoV-2 genomic surveillance and sequencing availability varied markedly across countries, with 63 countries performing routine genomic surveillance and 79 countries with high availability of SARS-CoV-2 sequencing. We also observed a marked heterogeneity of sequenced coverage across regions and countries. Across different variants, 21-46% of countries with explicit reporting on variants shared less than half of their variant sequences in public repositories. Our findings indicated an urgent need to expand sequencing capacity of virus isolates, enhance the sharing of sequences, the standardization of metadata files, and supportive networks for countries with no sequencing capability.

Orthogonal CRISPR-associated transposases for parallel and multiplexed chromosomal integration

Cell engineering is commonly limited to the serial manipulation of a single gene or locus. The recently discovered CRISPR-associated transposases (CASTs) could manipulate multiple sets of genes to achieve predetermined cell diversity, with orthogonal CASTs being able to manipulate them in parallel. Here, a novel CAST from Pseudoalteromonas translucida KMM520 (PtrCAST) was characterized without a protospacer adjacent motif (PAM) preference which can achieve a high insertion efficiency for larger cargo and multiplexed transposition and tolerate mismatches out of 4-nucleotide seed sequence. More importantly, PtrCAST operates orthogonally with CAST from Vibrio cholerae Tn6677 (VchCAST), though both belonging to type I-F3. The two CASTs were exclusively active on their respective mini-Tn substrate with their respective crRNAs that target the corresponding 5 and 2 loci in one Escherichia coli cell. The multiplexed orthogonal MUCICAT (MUlticopy Chromosomal Integration using CRISPR-Associated Transposases) is a powerful tool for cell programming and appears promising with applications in synthetic biology.

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization

The gut microbiota could affect human health and disease. Although disease-associated microbiota alteration has been extensively investigated in the Chinese population, a nationwide Chinese gut microbiota baseline is still lacking. Here we performed 16 S rRNA gene sequencing on fecal samples from 2678 healthy Chinese individuals, who belonged to eight ethnic groups and resided in 63 counties/cities of 28 provinces. We identified four enterotypes, three of which were enriched for Prevotella, Bacteroides, and Escherichia, respectively, whereas the fourth one had no dominant genus. By assessing the association between the gut microbiota and 20 variables belonging to six categories, geography, demography, diet, urbanization, lifestyle, and sampling month, we revealed that geography explained the largest microbiota variation, and clarified the distinct patterns in the associations with staple food type, ethnicity, and urban/rural residence. Specifically, the gut microbiota of Han Chinese and ethnic minority groups from the same sites was more alike than that of the same ethnic minority groups from different sites. Individuals consuming wheat as staple food were predicted to have more microbial genes involving in glucan 1,3-beta-glucosidase and S-adenosyl-L-methionine biosynthesis than those who consumed rice, based on functional prediction. Besides, an appreciable effect of urbanization on decreased intra-individual diversity, increased inter-individual diversity, and increased proportion of the Bacteroides enterotype was observed. Collectively, our study provided a nationwide gut microbiota baseline of the Chinese population and knowledge on important covariates, which are fundamental to translational microbiota research.

Long-Term Survival of Synechococcus and Heterotrophic Bacteria without External Nutrient Supply after Changes in Their Relationship from Antagonism to Mutualism

Marine phytoplankton and heterotrophic bacteria share a very close but usually changeable relationship. However, the ultimate fate of their unstable relationship on a long-term scale is unclear. Here, the relationship between Synechococcus and heterotrophic bacterial communities underwent a dramatic shift from antagonism to commensalism and eventually to mutualism during long-term cocultivation. The relationship change is attributed to the different (even opposite) effects of diverse bacterial members on Synechococcus and the ratio of beneficial to harmful bacteria. Different bacterial members also interact with each other (e.g., quorum-sensing communication, hostility, or mutual promotion) and drive a dynamic succession in the entire community structure that corresponds exactly to the shift in its relationship with Synechococcus. In the final mutualism stage, a self-sufficient nitrogen cycle, including nitrogen fixation, denitrification, and organic nitrogen degradation, contributed to the healthy survival of Synechococcus for 2 years without an exogenous nutrient supply. This natural selective trait of Synechococcus and heterotrophic bacteria toward mutualism under long-term coexistence provides a novel clue for understanding the ubiquity and competitive advantage of Synechococcus in global oceans.

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storage and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accepting data submissions from all over the world, and providing free open access to all publicly available data in support of worldwide research activities.

CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects

As immunotherapy is evolving into an essential armamentarium against cancers, numerous translational studies associated with relevant biomarkers, targets, and clinical effects have been reported in recent years. However, a large amount of associated experimental data remains unexplored due to the difficulty in accessibility and utilization. Here, we established a comprehensive high-quality database for cancer immunotherapy called CanImmunother (http://www.biomedical-web.com/cancerit/) through manual curation on 4515 publications. CanImmunother contains 3267 experimentally validated associations between 218 cancer sub-types across 34 body parts and 484 immunotherapies with 642 biomarkers, 108 targets, and 121 control therapies. Each association was manually curated by professional curators, incorporated with valuable annotation and cross references, and assigned with an association score for prioritization. To help clinicians and researchers in identifying and discovering better cancer immunotherapy and their respective biomarkers and targets, CanImmunother offers user-friendly web applications including search, browse, excel table, association prioritization, and network visualization. CanImmunother presents a landscape of experimental cancer immunotherapy association data, serving as a useful resource to improve our insight and to facilitate further discovery of advanced immunotherapy options for cancer patients.

FOSL2 Is Involved in the Regulation of Glycogen Content in Chicken Breast Muscle Tissue

The glycogen content in muscle of livestock and poultry animals affects the homeostasis of their body, growth performance, and meat quality after slaughter. FOS-like 2, AP-1 transcription factor subunit (FOSL2) was identified as a candidate gene related to muscle glycogen (MG) content in chicken in our previous study, but the role of FOSL2 in the regulation of MG content remains to be elucidated. Differential gene expression analysis and weighted gene coexpression network analysis (WGCNA) were performed on differentially expressed genes (DEGs) in breast muscle tissues from the high-MG-content (HMG) group and low-MG-content (LMG) group of Jingxing yellow chickens. Analysis of the 1,171 DEGs (LMG vs. HMG) identified, besides FOSL2, some additional genes related to MG metabolism pathway, namely PRKAG3, CEBPB, FOXO1, AMPK, and PIK3CB. Additionally, WGCNA revealed that FOSL2, CEBPB, MAP3K14, SLC2A14, PPP2CA, SLC38A2, PPP2R5E, and other genes related to the classical glycogen metabolism in the same coexpressed module are associated with MG content. Also, besides finding that FOSL2 expression is negatively correlated with MG content, a possible interaction between FOSL2 and CEBPB was predicted using the STRING (Search Tool for the Retrieval of Interacting Genes) database. Furthermore, we investigated the effects of lentiviral overexpression of FOSL2 on the regulation of the glycogen content in vitro, and the result indicated that FOSL2 decreases the glycogen content in DF1 cells. Collectively, our results confirm that FOSL2 has a key role in the regulation of the MG content in chicken. This finding is helpful to understand the mechanism of MG metabolism regulation in chicken and provides a new perspective for the production of high-quality broiler and the development of a comprehensive nutritional control strategy.

CNSA: a data repository for archiving omics data

With the application and development of high-throughput sequencing technology in life and health sciences, massive multi-omics data brings the problem of efficient management and utilization. Database development and biocuration are the prerequisites for the reuse of these big data. Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into six objects, namely Project, Sample, Experiment, Run, Assembly and Variation at present. Moreover, CNSA has created a correlation model of living samples, sample information and analytical data on some projects. Both living samples and analytical data are directly correlated with the sample information. From either one, information or data of the other two can be obtained, so that all data can be traced throughout the life cycle from the living sample to the sample information to the analytical data. Complying with the data standards commonly used in the life sciences, CNSA is committed to building a comprehensive and curated data repository for storing, managing and sharing of omics data. We will continue to improve the data standards and provide free access to open-data resources for worldwide scientific communities to support academic research and the bio-industry. Database URL: https://db.cngb.org/cnsa/.

2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV

Since the COVID-19 epidemic is still expanding around the world and poses a serious threat to human life and health, it is necessary for us to carry out epidemic transmission prediction, whole genome sequence analysis, and public psychological stress assessment for 2019-nCoV. However, transmission prediction models are insufficiently accurate and genome sequence characteristics are not clear, and it is difficult to dynamically assess the public psychological stress state under the 2019-nCoV epidemic. Therefore, this study develops a 2019nCoVAS web service (http://www.combio-lezhang.online/2019ncov/home.html) that not only offers online epidemic transmission prediction and lineage-associated underrepresented permutation (LAUP) analysis services to investigate the spreading trends and genome sequence characteristics, but also provides psychological stress assessments based on such an emotional dictionary that we built for 2019-nCoV. Finally, we discuss the shortcomings and further study of the 2019nCoVAS web service.

Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts

BACKGROUND

Cigar wrapper leaves are the most important raw material of cigars. Studying the genomic information of cigar tobacco is conducive to improving cigar quality from the perspective of genetic breeding. However, no reference genome or full-length transcripts at the genome-wide scale have been reported for cigar tobacco. In particular, anion channels/transporters are of high interest for their potential application in regulating the chloride content of cigar tobacco growing on coastal lands, which usually results in relatively high Cl- accumulation, which is unfavorable. Here, the PacBio platform and NGS technology were combined to generate a full-length transcriptome of cigar tobacco used for cigar wrappers.

RESULTS

High-quality RNA isolated from the roots, leaves and stems of cigar tobacco were subjected to both the PacBio platform and NGS. From PacBio, a total of 11,652,432 subreads (19-Gb) were generated, with an average read length of 1,608 bp. After corrections were performed in conjunction with the NGS reads, we ultimately identified 1,695,064 open reading frames including 21,486 full-length ORFs and 7,342 genes encoding transcription factors from 55 TF families, together with 2,230 genes encoding long non-coding RNAs. Members of gene families related to anion channels/transporters, including members of the SLAC and CLC families, were identified and characterized.

CONCLUSIONS

The full-length transcriptome of cigar tobacco was obtained, annotated, and analyzed, providing a valuable genetic resource for future studies in cigar tobacco.

Whole-exome sequencing of alpha-fetoprotein producing gastric carcinoma reveals genomic profile and therapeutic targets

Alpha-fetoprotein producing gastric carcinoma (AFPGC) is a rare and aggressive subtype of gastric cancer. However, little is known about the genomic features of this disease. We perform whole-exome sequencing analysis of AFPGC, and identify 34 significantly mutated genes. Somatic copy number alterations analysis reveals several significant focal amplifications (e.g. 19q12, 17q12) and focal deletions (e.g. 1p36.11, 9p21.3), and some of these negatively affect the patient prognosis. Comparative analyses reveal that AFPGC has distinct genomic features from gastric cancer of The Cancer Genome Atlas as well as four molecular subtypes. Several frequently altered genes with potential as therapeutic targets are identified in AFPGC. Further analysis reveals that AFPGC with amplification of CCNE1 at 19q12 and/or ERBB2 at 17q12 show poorer survival and more aggressive. Subsequently, based on our established patient-derived xenograft models for AFPGC, translational research is performed and the therapeutic value of targeting CCNE1 and ERBB2 is validated. In this work, we provide an understanding of genomic characteristics of AFPGC and propose a platform to explore and validate the genome-guided personalized treatment for this disease.

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China-association with asthma, rhinitis and rhinoconjunctivitis in high school students

BACKGROUND

Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries.

METHODS

Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms.

RESULTS

Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut.

CONCLUSIONS

We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects. Video abstract.

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19

The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated 16 of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19.

Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum (Fagopyrum) tibeticum. Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum (Fagopyrum) tibeticum, Atraphaxis bracteata and Calligonum ebinuricum. Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum (Fagopyrum) tibeticum, A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum. Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum, which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.

Effect of liquid volume and microflora source on degradation rate and microbial community in corn stover degradation

Degradation is the bottleneck in the utilization of crop straw. In this paper, we screened the microbial consortia degrading corn stover from straw degrading consortia MC1 (M), sheep feces (Y), and mixtures (Q) of M, Y, and cattle feces. The effects of microflora source and liquid volume (representing dissolved oxygen) on the microbial community and degradation rate of corn stover were investigated. The results showed that the degradation rate and cellulase activity of a 200 mL liquid volume (L2) were significantly higher than that of 100 mL (L1). Microflora source had a significant effect on bacterial and fungal diversity, composition and taxa. Q and Y had higher bacterial and fungal α-diversity than that of M. The degradation rate was significantly correlated with cellulase activity but not with microbial diversity. This indicated that liquid volume had a significant effect on degradation rate while microflora source had a significant effect on microbial community in corn stover degradation.

Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses

Background

The pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Some of the studies on aspects of SARS-CoV-2 cell entry and innate immunity have produced seemingly contradictory claims. In this situation, a comprehensive comparative analysis of a large number of related datasets from several studies could bring more clarity, which is imperative for therapy development.

Methods

We therefore performed a comprehensive comparative study, analyzing RNA-Seq data of infections with SARS-CoV-2, SARS-CoV and MERS-CoV, including data from different types of cells as well as COVID-19 patients. Using these data, we investigated viral entry routes and innate immune responses.

Results and Conclusion

First, our analyses support the existence of cell entry mechanisms for SARS and SARS-CoV-2 other than the ACE2 route with evidence of inefficient infection of cells without expression of ACE2; expression of TMPRSS2/TPMRSS4 is unnecessary for efficient SARS-CoV-2 infection with evidence of efficient infection of A549 cells transduced with a vector expressing human ACE2. Second, we find that innate immune responses in terms of interferons and interferon simulated genes are strong in relevant cells, for example Calu3 cells, but vary markedly with cell type, virus dose, and virus type.

SIRT3 consolidates heterochromatin and counteracts senescence

Sirtuin 3 (SIRT3) is an NAD⁺-dependent deacetylase linked to a broad range of physiological and pathological processes, including aging and aging-related diseases. However, the role of SIRT3 in regulating human stem cell homeostasis remains unclear. Here we found that SIRT3 expression was downregulated in senescent human mesenchymal stem cells (hMSCs). CRISPR/Cas9-mediated depletion of SIRT3 led to compromised nuclear integrity, loss of heterochromatin and accelerated senescence in hMSCs. Further analysis indicated that SIRT3 interacted with nuclear envelope proteins and heterochromatin-associated proteins. SIRT3 deficiency resulted in the detachment of genomic lamina-associated domains (LADs) from the nuclear lamina, increased chromatin accessibility and aberrant repetitive sequence transcription. The re-introduction of SIRT3 rescued the disorganized heterochromatin and the senescence phenotypes. Taken together, our study reveals a novel role for SIRT3 in stabilizing heterochromatin and counteracting hMSC senescence, providing new potential therapeutic targets to ameliorate aging-related diseases.

Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome

Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. Our results provided a chromosome-level high-quality genome assembly with a predicted genome size of 542.6 Mbp (2n = 40) and a scaffold N50 of 24.9 Mbp. The BUSCO value for genome assembly completeness was higher than 96%, and the single-base accuracy was 99.997%. Based on EVM-StringTie genome annotation, a total of 19,147 protein-coding genes were identified, including 35,093 mRNA transcripts. In addition, a novel gene-finding strategy named RNR was introduced, and in total, 51 (82) novel genes (transcripts) were identified. Lastly, we present here the first reference genome for Trachidermus fasciatus; this sequence is expected to greatly facilitate future research on this species.

Research on the Species Difference of the Hepatotoxicity of Medicine Based on Transcriptome

In recent years, several drugs have been withdrawn from use by regulatory bodies owing to hepatotoxicity; therefore, studies on drug-induced liver injury (DILI) are being actively pursued. Most studies evaluating DILI use rats or mice as animal models to determine drug toxicity; however, the toxicity of a drug can vary between rats or mice. These inconsistencies in in vivo studies among different animal models affect the extrapolation of experimental results to humans. Thus, it is particularly important to choose the most suitable animal model to determine drug hepatotoxicity owing to the genomic differences between rats and mice resulting from evolution. In this study, genome-wide transcriptome analysis was used to explore hepatotoxicity caused by differences in species. Our findings provide the preclinical basis to further study the mechanisms of drug hepatotoxicity and aid in the selection of animal models to determine drug safety. We used murine models (Sprague-Dawley and Wistar rats, ICR and Kunming mice) in this study and by using transcriptome sequencing with the differentially expressed genes in rat and mouse livers as the entry point, we explored the mechanism of oxidative stress and the difference in gene expression in the lipid-metabolism pathway between rats and mice. The clinically established hepatotoxic drugs, fructus psoraleae and acetaminophen were used to validate our study. Using pathological studies, we confirmed that oxidative stress in mice was more serious than that in rats, and that Kunming mice were more suited for the study of oxidative stress-related DILI. The validity of our findings was further verified based on gene expression. Thus, our study could serve as a valuable reference for the evaluation of potential preclinical hepatotoxicity. Moreover, it could be used in the prediction and early diagnosis of drug-induced liver injury caused by traditional Chinese medicine or synthetic drugs, thereby providing a new avenue for drug-toxicity studies.

Genetic Polymorphism Drives Susceptibility Between Bacteria and Bacteriophages

Phage therapy has attracted much attention for the treatment of antibiotic-resistant bacteria in recent years. However, it is common for bacteria to obtain resistance capability in short time after interaction with a lytic phage, as observed in phage therapy and co-culture of host and phage in a lab. In order to understand the mechanisms behind resistance, Staphylococcus aureus AB91118 and its lytic phage LQ7 were studied as a model system. A mutant strain named R1-3-1 resistant to the ancestral phage LQ7 was isolated, and then phages experimentally evolved from LQ7 were able to kill R1-3-1. Genomes of the two bacterial strains and the three phages (LQ7, ELQ7P-10, and ELQ7P-20) were analyzed based on deep sequencing data of NGS. Analyses showed that a few mutations could be identified in R1-3-1 and the evolved phages. Instead, in all the genomes of the bacteria and the phages, there exists genetic polymorphism of minor alleles, which distributes in many functional genes. Specifically, in the AB91118-LQ7 system it was found that the unique polymorphism sites in R1-3-1 associated to metabolic pathways could be inhibited by chloramphenicol (CHL). The resistant mutant R1-3-1 could become sensitive to the phage LQ7 in the presence of CHL. Combined use of CHL and the evolved phage from 20 cycles (ELQ7P-20) could produce the least resistance when killing the bacteria AB91118. The genetic polymorphism of minor alleles would be a new mechanism to drive the co-evolution between a phage and its host, which may enable the phage and the host get ready and fast response to the selective pressure from one to the other.

The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

BACKGROUND

Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far.

RESULTS

The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation.

CONCLUSIONS

The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.